The High Level SBW Libraries

1. The High Level SBW Libraries Andrew Finney, Herbert Sauro, Mike Hucka and Hamid Bolouri ERATO Kitano Systems Biology Workbench Project

2. Overview Tutorial 1 Application Tutorial 2 Application edu.caltech.trigonometry Service Trig • 3 Tutorials in Java and C++: • Calling a known service • Implementing a service • Finding services in a known category • Assumes some understanding of Java or C++ SBW Broker SBW Interface SBW Interface

3. Tutorial 1: Calling a known Service • Assume we know there is • a module “edu.caltech.trigonometry” • with a service “Trig” • Which has the methods • double sin(double) • double cos(double) • We will call the sin method

4. Tutorial 1: Accessing a service in C++ and Java • In Java: Module module = SBW.getModuleInstance(“edu.caltech.trigonometry”); Service service = module.findServiceByName(“Trig”); • In C++: Module module = SBW::getModuleInstance(“edu.caltech.trigonometry”); Service service = module.findServiceByName(“Trig”);

5. Tutorial 1: Calling a method in Java • Create interface for service: Interface Trigonometry { double sin(double x) throws SBWException; double cos(double x) throws SBWException; } • Create proxy with this interface and call it: Trigonometry trig = (Trigonometry)service.getServiceObject( Trigonometry.class); Double result = trig.sin(x);

6. Tutorial 1: Calling a method in C++ • Access Method object: Method method = service.getMethod(“sin”); • Invoke method, marshalling arguments and result: DataBlockReader resultData = method.call(DataBlockWriter() << x); SBWDouble result ; resultData >> result ;

7. Tutorial 1: Exception Handling Exception Exception • Most High Level API calls can potentially throw SBWException • SBWException base class of hierarchy of exception types • SBWApplicationException can be thrown by service implementations Error Message Error Message SBW

8. Tutorial 1: Summary • Start with information on a specific service • Access module then service • Call Method • In Java: use proxy object with defined interface • In C++: use call on Method object • Exception Handling

9. Tutorial 2: Implementing a Service • Implementation of the service called in Tutorial 1 • Service is an interface to a software resource inside a module (executable) • Typically an executable operates in 3 modes: • Normal • Register • Module

10. Tutorial 2: Java Service Implementation class Trig { public double sin(double x) throws SBWApplicationException { return Math.sin(x); } public double cos(double x) throws SBWApplicationException { return Math.cos(x); } }

11. Tutorial 2: Java main method ModuleImpl moduleImp = new ModuleImpl( “edu.caltech.trigonometry”, “trig”, SBW.STATIC, this.getClass()); moduleImp.addService( “trig funcs”, “trigonometry”, Trig.class); if (args[0].equals(“-sbwregister”)) moduleImp.register(); else (args[0].equals(“-sbwmodule”)) moduleImp.enableServices(); else // in normal mode – do something else

12. Tutorial 2: C++ Service Implementation class Sin : public Handler { DataBlockWriter receive( Module from, DataBlockReader args) throws SBWApplicationException { SBWDouble x; args >> x ; return DataBlockWriter() << sin(x); } }; class Cos : public Handler …

13. Tutorial 2: C++ main function ModuleImpl moduleImp( “edu.caltech.trigonometry”, “trig”, SBW::STATIC, argv[0]); moduleImp.addService(“Trig”, “trig funcs”, “trigonometry”); if (strcmp(argv[1], “-sbwregister”) == 0) moduleImp.register(); else if (strcmp(argv[1], “-sbwmodule”) == 0) { moduleImp.setHandler( “trig”, new Sin(), “double sin(double)”); moduleImp.setHandler( “trig”, new Cos(), “double cos(double)”); moduleImp.enableServicesAndWait(); } else // normal mode – do something else

14. Tutorial 2: Summary • Create Service implementation • In Java: use normal class • In C++: one class per method • Supply module information in ModuleImpl constructor • Supply service implementation via addService method on ModuleImpl • Use the register method in register mode • Use the enableServices method in module mode

15. Tutorial 3: Finding and using services in a given category • Dynamically locate services in a given category • We will locate services in the “Analysis” category • This category is an important standard for SBW • Has one method: • void doAnalysis(string sbml)

16. Tutorial 3: Finding services in Java • Get information on services in category: ServiceDescriptor[] descriptors = SBW.findServices(“Analysis”); • Access the humanly readable name of a service: descriptors[0].getDisplayName(); • Get a real service: Service service = descriptors[0].getServiceInModuleInstance();

17. Tutorial 3: Finding services in C++ • Get information on services in category: std::vector<ServiceDescriptor> *descriptors = SBW::findServices(“Analysis”); • Access the humanly readable name of a service: (*descriptors)[0].getDisplayName(); • Get a real service: Service service = (*descriptors)[0].getServiceInModuleInstance();

18. Tutorial 3: Summary • Start with just a service category and its interface • Use findServices to get static information on potential services • Perhaps display list of potential services to user using getDisplayName • Access actual service, perhaps via user selection, using getServiceInModuleInstance

19. Summary • Refer to “Programmer’s Manual for the Systems Biology Workbench (SBW)” Finney et al for more detail • http://www.cds.caltech.edu/erato/sbw/docs/api • Subject to change: implementation not complete • Scripting language High Level APIs similar to those described in this presentation